{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T10:49:01Z","timestamp":1788173341016,"version":"build-2803163510"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2018,5,14]],"date-time":"2018-05-14T00:00:00Z","timestamp":1526256000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"European Molecular Biology Laboratory","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>One goal of synthetic biology is to make new enzymes to generate new products, but identifying the starting enzymes for further investigation is often elusive and relies on expert knowledge, intensive literature searching and trial and error.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Transform Molecules in Enzyme Reactions, an online computational tool that transforms query substrate molecules into products using enzyme reactions. The most similar native enzyme reactions for each transformation are found, highlighting those that may be of most interest for enzyme design and directed evolution approaches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/www.ebi.ac.uk\/thornton-srv\/transform-miner<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty394","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T19:13:34Z","timestamp":1525893214000},"page":"3597-3599","source":"Crossref","is-referenced-by-count":15,"title":["Transform-MinER: transforming molecules in enzyme reactions"],"prefix":"10.1093","volume":"34","author":[{"given":"Jonathan D","family":"Tyzack","sequence":"first","affiliation":[{"name":"EMBL-EBI, Wellcome Genome Campus, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antonio J M","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"EMBL-EBI, Wellcome Genome Campus, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neera","family":"Borkakoti","sequence":"additional","affiliation":[{"name":"EMBL-EBI, Wellcome Genome Campus, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janet M","family":"Thornton","sequence":"additional","affiliation":[{"name":"EMBL-EBI, Wellcome Genome Campus, Cambridge, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,5,14]]},"reference":[{"key":"2023012712420610900_bty394-B1","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1021\/ci034207y","article-title":"Molecular similarity searching using atom environments, information-based feature selection, and a Na\u00efve Bayesian classifier","volume":"44","author":"Bender","year":"2004","journal-title":"J. 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Ed"},{"key":"2023012712420610900_bty394-B11","article-title":"RDKit","author":"Landrum","year":"2018","journal-title":"Open-Source Cheminformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/20\/3597\/48918993\/bioinformatics_34_20_3597.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/20\/3597\/48918993\/bioinformatics_34_20_3597.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:34:58Z","timestamp":1674826498000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/20\/3597\/4995847"}},"subtitle":[],"editor":[{"given":"Jonathan","family":"Wren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,14]]},"references-count":11,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2018,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty394","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,10,15]]},"published":{"date-parts":[[2018,5,14]]}}}